We prove several results about substructures in Latin squares. First, we explain how to adapt our recent work on high-girth Steiner triple systems to the setting of Latin squares, resolving a conjecture of Linial that there exist Latin squares with arbitrarily high girth. As a consequence, we see that the number of order-n Latin squares with no intercalate (i.e., no 2 × 2 Latin subsquare) is at least EN , where N is the number of intercalates in a uniformly random order-n Latin square.In fact, extending recent work of Kwan, Sah, and Sawhney, we resolve the general large-deviation problem for intercalates in random Latin squares, up to constant factors in the exponent: for any constant 0 < δ ≤ 1 we have Pr[N ≤ (1 − δ)EN] = exp(−Θ(n 2 )) and for any constant δ > 0 we haveFinally, we show that in almost all order-n Latin squares, the number of cuboctahedra (i.e., the number of pairs of possibly degenerate 2 × 2 subsquares with the same arrangement of symbols) is of order n 4 , which is the minimum possible. As observed by Gowers and Long, this number can be interpreted as measuring "how associative" the quasigroup associated with the Latin square is.