Cortinarius iodes produces a rusty-brown spore print. Spores are elliptical, with a finely roughened surface, measuring 8–10 by 5–6.5 μm. The basidia (spore-bearing cells) are four-spored, club-shaped, and measure 28–39.5 by 9.3–14 μm. Both cheilocystidia and pleurocystidia are absent from the hymenium; the gill edge is populated by basidia and their undeveloped equivalents, basidioles. The cap cuticle comprises a distinctive layer of 3–8 μm-wide hyphae that form a layer usually 110–125 μm thick; this layer is less distinct or thinner in old or poorly preserved specimens. Clamp connections are present in hyphae throughout the fruit body.
