Atypical mycobacteria comprise an uncommon heterogenous non-tuberculous group of acid-fast bacteria that rarely involve skin. The pattern of atypical mycobacterial cutaneous infections (AMCI) has not been previously studied in Egypt. The aim of this study was to describe the clinical characteristics, pathological features and species profile of AMCI among Egyptian patients. A retrospective study included 46 cases, diagnosed with AMCI during the period 2002 to 2012. The study included 34 males (73.9%) and 12 females (26.9%). The average age of patients was 39 years while the average duration of lesions was 15 months. The lesions were mostly located on the extremities (91.3%) and there was predominance of single (65.2%) and nodular (41.4%) lesions. History of trauma was confirmed in 91.3%. Histologically, the granulomas were mostly superficial (67.4%) with predominance of nodular suppurative pattern (84.8%). Other significant histological findings included epidermal hypertrophy (100%), presence of large-sized multinucleated giant cells (87%) and intrafollicular neutrophilic abscesses (84.8%). The diagnosis was proved by direct smear in 6.5%, skin biopsy in 10.9%, tissue culture in 47.8% and polymerase chain reaction (PCR) in 34.8%. Isolated species included Mycobacterium marinum (84.8%), Mycobacterium fortuitum (10.9%) and Mycobacterium kansasii (4.3%). Although the results of this study recommend that the diagnosis of AMCI is based mainly on culture and PCR, other clinicopathological features such as history of trauma, acral location of the lesion and suppurative granulomatous reaction with intrafollicular abscesses could be helpful clues in suspecting AMCI.