Clostridium spore counts, sugars and organic acids were investigated in 52 Manchego cheeses with different degrees of late blowing defect (LBD) and in 25 Manchego cheeses without LBD. Cheeses with LBD showed significantly higher spore counts, lower levels of lactose, galactose, citric and lactic acids, and higher levels of acetic and butyric acids than cheeses without LBD. The same effect of LBD on sugars and organic acids, with the exceptions of galactose and propionic acid, was recorded for raw milk (RM) and pasteurized milk (PM) Manchego cheeses. Galactose concentration was significantly lower in PM cheeses with LBD than in PM cheeses without LBD, but no significant differences were found between RM cheeses with and without LBD. Propionic acid content was significantly lower in RM cheeses with LBD, and significantly higher in PM cheeses with LBD, than in the respective cheeses without LBD. © 2012 Elsevier Ltd.