The controversy about the validity of using bone and tooth mineral (biological apatite) as an alternative sample material to collagen for stable carbon isotope analysis is briefly reviewed. Some of the apparent contradictions may have arisen as a result of the effects of different pretreatment methods, as well as the choice of tissue. Experimental results are presented which document the isotopic and mineralogical effects of 1 M acetic acid pretreatment on modern and fossil biological apatites. The data show that this procedure has marked effects on modern mineral. Prolonged reaction in 1 M acetic leads to recrystallization of bone apatite to brushite (dicalcium phosphate-dihydrate), suggesting that this treatment must be used cautiously for recent archaeological materials. Recrystallization was not observed for older fossil material; changes are rather due to elimination of calcite and the more soluble apatite crystallites. The results indicate that enamel provides the most consistent results. Accordingly, only enamel was used for an applied study of the diets of 1.8 Ma extinct primates from Swartkrans Cave, South Africa.