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Crystal Inclusions: How Things Get Inside a Crystal, and What They Prove

By Digital Towns Crystals · Last reviewed October 8, 2026

Short answer: an inclusion is any material sealed inside a crystal: another mineral, a droplet of the fluid the crystal grew from, a gas bubble, or a hollow. It gets there in one of three ways. It existed first and was engulfed, it grew at the same time and was overgrown, or it separated out of the host after growth. Quartz is the best recorder of all, because it seals its inclusions so well that scientists use them to read the temperature and chemistry of long-vanished fluids.

What counts as an inclusion?

Gemologists use the word for every internal feature that is not the host crystal itself: solid crystals, liquid-filled cavities, gas, cracks that resealed into veils, and growth zones. Collectors use it more narrowly for the visible things, the needles, mosses and bubbles that make a specimen interesting. Both meanings are right. The useful question is not "does it have inclusions?" (nearly every natural crystal does) but "what are they, and when did they get there?"

That second question has a precise answer in the mineralogical literature, summarized well by The Quartz Page's chapter on inclusions, which sorts them by timing.

How do inclusions get into a crystal?

1. Protogenetic: the guest arrived first

Some minerals formed before the host and were simply swallowed as the host grew around them. The giveaway is randomness: included fibers that run through the entire crystal at random orientations are typical examples. In rock crystals from the Tipling area in Nepal, gray-green actinolite fibers run in all directions, and because the quartz shows no growth disruption around them, the fibers very likely predate it.

Titanium oxides show the timing logic nicely. Rutile forms at moderate and high temperatures, so it tends to sit deep inside quartz or run through whole crystals, having formed first. Anatase, the low-temperature form of the same compound, tends to form later and often grows on the crystal faces instead. Same chemistry, different moment, different position. The rutilated quartz guide covers the golden-needle stone itself.

2. Syngenetic: host and guest grew together

When both minerals crystallize at the same time, they compete for space, and the included mineral is often distorted, sometimes beyond recognition. This is the hardest group to identify without instruments. A special case is a growth pause during which another mineral coats the faces before the host resumes: that produces a phantom, the subject of the phantom quartz guide.

3. Epigenetic: the guest came out of the host

Some elements fit into a crystal's lattice at high temperature but not at low. As the crystal cools, they separate out as new microscopic crystals, a process called exsolution. These inclusions are very often oriented along the host's crystal axes. The Quartz Page names rose quartz as the best example of quartz with epigenetic inclusions; its color comes from fibrous inclusions, which the International Gem Society describes as a mineral similar to dumortierite. Oriented exsolved needles are also what make stars and silk in other gems.

How are fluid inclusions trapped, and why is there a bubble?

Most quartz grows from hot water, so water is the most common thing it traps. Almost all quartz crystals contain small amounts of fluid in inclusions, but usually the cavities are microscopically small. Many rock crystals have a cloudy or milky base because of myriads of small bubbles.

The process, step by step:

  1. Trapping. A growing face develops an irregularity, often when growth is fast. Skeletal crystals, where the edges grow faster than the face centers, are especially prone to sealing pockets of fluid this way.
  2. Shaping. Over time the cavity adjusts to the host's structure and can take the form of a "negative crystal", a hollow with crystal faces that is always oriented parallel to the host.
  3. Cooling. The fluid was sealed in at the growth temperature. On cooling it contracts, and a vapor bubble appears in the space left behind. A cavity with liquid plus vapor is a two-phase inclusion; add a tiny salt crystal and it is three-phase.
  4. Reading it back. Heat the crystal under a microscope until the bubble disappears, and you recover an estimate of the trapping temperature. This is the basis of fluid inclusion research, and quartz is its favorite material because it is chemically stable and seals what it traps almost perfectly.

Not all fluids are water. Carbon dioxide and methane, both gases at normal pressure, can be enclosed as liquids at very high pressures during crystal formation, and some quartz contains petroleum and bitumen.

What do inclusions say about temperature?

Real numbers from the record:

Setting What inclusions and occurrence show
Milky "Suttrop-type" quartz, Sauerland, Germany Growth temperature rose from about 60 to 80 °C to above 120 °C; fluid inclusions take up to 10% of the volume
General quartz growth Crystals rarely reach significant size below about 100 to 150 °C
Pegmatite fluids 400 to 800 °C
Large, slow-grown Alpine rock crystals Salt-rich fluids in the core, more carbon dioxide toward the rim

The Suttrop figure comes from The Quartz Page's milky quartz chapter, and the growth and pegmatite figures from its occurrence chapter. The milky quartz case shows a practical side effect: with that many fluid inclusions, the crystals have a lower specific gravity than usual.

What do inclusions look like in a specimen?

You see Likely inclusion Timing
Straight needles crossing the whole crystal Rutile, tourmaline, actinolite Usually protogenetic
Green moss or layers near the base Chlorite Late, low temperature
A ghost of the crystal tip Phantom layer of another mineral or a color zone Growth pause
Silky sheen, pink color Exsolved fibers Epigenetic
Moving bubble in a cavity Water and vapor (enhydro) Syngenetic
Red flakes in amethyst Hematite Varies

The last row hides a classic mislabel. Red flakes in amethyst and the red inclusions of strawberry quartz were long described as lepidocrocite, but analysis found them to be hematite, and the Quartz Page suggests most "lepidocrocite inclusions" in the literature are actually hematite.

Which misconceptions should you drop?

  • "Inclusions lower the value." True for faceted gems prized for clarity, false for specimens and many cut stones where the inclusion is the point.
  • "Yellow from iron inclusions makes it citrine." Deep yellow quartz stained by iron compounds is not citrine; natural citrine's color comes from trace elements built into the quartz lattice, not from included iron minerals.
  • "A bubble means it is glass." Glass has round gas bubbles, but natural quartz has bubbles too, inside flat, angular liquid-filled cavities. The shape of the cavity, not the bubble, is the tell.
  • "Inclusions are flaws to be removed." They are protected samples. Minerals that would otherwise be altered or dissolved survive because the quartz around them shields them from aggressive fluids.

Do labs use inclusions?

Constantly. The International Gem Society lists color zoning, twinning, two and three phase inclusions and negative crystals among the identifying characteristics of natural quartz. Inclusions are also the first place to look for treatments: GIA's 2024 review of gem fluorescence shows how surface-reaching glass filler in clarity-enhanced rubies can fluoresce blue against the ruby's red glow. The fluorescence guide covers that light.

What to look for when you buy included quartz

Use a 10x loupe and a single strong light behind the stone. Ask three things: what is the inclusion (a seller should name it), is it sealed or does it reach the surface (surface-reaching inclusions are soft spots and filler entry points), and does its geometry make sense (needles straight, phantoms parallel to faces, fluid cavities angular).

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Frequently asked questions

What is an inclusion in a crystal?

Any material enclosed inside a crystal: another mineral, a droplet of liquid, a gas bubble or a cavity. Inclusions form before, during or after the host crystal grows, and their shape and position show which.

How do inclusions get inside quartz?

Three ways: the host engulfs a mineral that formed first, the host and guest grow together, or elements separate out of the host as it cools. Fluids are trapped when a growing face seals off a small pocket of the solution.

Why does the bubble in enhydro quartz move?

The cavity holds liquid plus a vapor bubble that formed when the trapped fluid cooled and contracted. If the cavity is large enough, the bubble floats to the highest point as you tilt the crystal.

Do inclusions make a crystal less valuable?

Not for most specimens. Clarity matters in faceted gems, but in specimen quartz well-formed needles, phantoms, gardens and moving bubbles usually add value, especially when they are sharp, sealed and attractively placed.

Can inclusions tell you how hot a crystal formed?

Yes. Fluid inclusions trapped as a single phase at high temperature separate into liquid and vapor on cooling. Reheating until they rejoin gives an estimate of the trapping temperature, which is a standard technique in geology.

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