Microdissection testicular sperm extraction (micro-TESE) was developed to minimize the testicular injury associated with multiple open TESEs. We sought to evaluate a mini-incision micro-TESE in men with cryptozoospermia and non-obstructive azoospermia (NOA). We conducted a retrospective study of 26 consecutive men with NOA and cryptozoospermia who underwent a primary (first) micro-TESE between March 2015 and August 2015. Final assessment of sperm recovery (reported on the day of intra-cytoplasmic sperm injection (ICSI)) was recorded as (i) successful (available spermatozoa for ICSI) or (ii) unsuccessful (no spermatozoa for ICSI). The decision to perform a mini-incision micro-TESE (with limited unilateral micro-dissection) or standard/extensive (with unilateral or bilateral micro-dissection) was guided by the intra-operative identification of sperm recovery (≥5 spermatozoa) from the first testicle. Overall, sperm recovery was successful in 77% (20/26) of the men. In 37% of the men (8/26), the mini-incision micro-TESE was successful (positive sperm recovery). The remaining 18 men required a standard (extensive) microdissection: 61% (11/18) underwent a unilateral and 39% (7/18) a bilateral micro-TESE. We found that 90% (9/10) of the men with cryptozoospermia and 63% (10/16) of the men with NOA underwent a unilateral (mini or standard micro-TESE). The mini-incision micro-TESE allowed for successful sperm recovery in 60% (6/10) of the men with cryptozoospermia and 13% (2/16) of the men with NOA. The data demonstrate that a mini-incision micro-TESE together with rapid intra-operative assessment and identification of spermatozoa recovery can be useful in men undergoing microTESE, particularly, men with cryptozoospermia.