Tartrate-resistant acid phosphatase (TRAP) consists of 2 structurally related isoforms, 5a and 5b, and the latter has been characterized as containing a sugar moiety devoid of sialic acid(s). We provide evidence of a greater difference between the sugar moieties of the two isoforms than the presence of sialic acid(s) in TRAP 5a. TRAP 5a and 5b were highly purified from human blood and femur extracts, respectively, and after purifying the TRAPs by successive chromatography on a series of lectin affinity columns, we used the chromatographs obtained to estimate the composition of their sugar chain structure and found that both TRAP 5a and 5b had contained the heterogenous sugar chains. More specifically, TRAP 5a mainly contained a high-mannose-type sugar chain, while TRAP 5b had multi-antennary complex-type sugar chain. These results indicate that the differences between TRAP 5a and 5b consist not only of a difference in modification by sialic acid but differences in other sugar chain structures. These differences are involved in an extraordinary enzyme maturation process since the carbohydrate chains cover the repressive loop where the proteolytic site is located.