The relationship between the genes controlling heart and adipose lipoprotein lipase in fasted animals has been studied. 32 inbred mouse strains were tested for variations in heart or adipose specific activity and thermolability. The survey revealed that specific activity of heart and adipose lipoprotein lipase varied as much as 3-fold and 20-fold, respectively. In thermolability, up to a 2-fold variation was observed in the lipase in each tissue. The correlation coefficient between variations in heart and adipose lipase was apparently not significant for both parameters studied. Additional studies were performed in two strains, BALB/c and C57BL/6, along with the recombinant inbred set derived from them. The two strains did not show genetic variation for lipoprotein lipase thermolability, although the inactivation rate of heart lipase was higher than that of adipose lipase. However, BALB/c and C57BL/6 displayed significant differences in their levels of lipoprotein lipase specific activity. Thus, strain C57BL/6 showed higher heart activity when compared to BALB/c, whereas the latter showed higher adipose lipase activity when compared to C57BL/6, i.e. an inverse relationship. The specific activity levels of heart and adipose lipoprotein lipase in the recombinant inbred strains derived from BALB/c and C57BL/6 exhibited independent inheritance. Thus, in adipose tissue, a single major gene seems to control the variation observed, while the inheritance pattern of heart activity could imply involvement of more than one gene. Moreover, two out of the seven recombinant strains showed distinct recombinant phenotypes, indicating that separate unlinked genes control the variations found in heart and adipose activity. We conclude that the expression of heart and adipose lipoprotein lipase activity is under independent genetic control.