In this study we describe a method for obtaining reliable estimates of standard metabolic rate for small ectothermic animals. Using repeated stop-flow respirometry we were able to investigate the effects of inbreeding on standard metabolic rate in Drosophila melanogaster. We hypothesized that inbreeding results in increased metabolic rate, and further that this effect would be more pronounced at stressful low and high temperatures. However, contrary to our hypothesis we did not find any interaction between temperature and the effect of inbreeding or any general difference in metabolic rate between inbred and outbred individuals. However, inbreeding did affect the variance. Nonetheless variance in metabolic rate was higher between the inbred lines compared to the outbred lines with some inbred lines having very high or low metabolic rate, indicating that genetic drift, and not inbreeding, seem to explain the variation in metabolic rate in populations of different size.