Several studies support of the use of testicular rather than ejaculated spermatozoa for intracytoplasmic sperm injection (ICSI) in couples with virtual azoospermia or cryptozoospermia, although this approach remains controversial. We sought to evaluate sperm retrieval outcomes with microdissection testicular sperm extraction (micro-TESE) in men with cryptozoospermia. We conducted a retrospective study of 24 consecutive micro-TESEs in men with cryptozoospermia. We also evaluated the outcomes of seven consecutive TESAs (testicular sperm aspiration) in cryptozoospermic men during the same time period (January 2007 and September 2014). Micro-TESE and TESA were performed on the day prior to ICSI. Final assessment of sperm recovery (reported on the day of ICSI) was recorded as (i) successful (available spermatozoa for ICSI) or (ii) unsuccessful (no spermatozoa for ICSI). The decision to perform a unilateral or bilateral micro-TESE was guided by the intra-operative evaluation of sperm recovery from the first testicle. A unilateral procedure was performed in 87.5% (21/24) and 57% (4/7) of the micro-TESE and TESA cohorts, respectively. Sperm recovery was successful in 96% (23/24) of the men who underwent micro-TESE and 43% (3/7) of the men who underwent TESA (p < 0.01). The ICSI pregnancy rates (per embryo transfer) in the micro-TESE and TESA groups were comparable [33% (6/18) and 50% (1/2), respectively]. The data indicate that micro-TESE is a highly successful sperm retrieval technique for men with cryptozoospermia and few of these men will require a bilateral procedure. Moreover, sperm retrieval rates are higher with micro-TESE than TESA in this group of men.