Animals’ capability to absorb energy and nutrients from food poses a major internal constraint that affects the amount of resources available for allocation to maintenance, growth, signaling, and reproduction. Intestinal surface is the largest area of contact between immune system and microbial antigens; gut thus appears the main arena where trade‐offs between immune function and other components of fitness arise. Assessment of the integrity of digestive machinery should therefore be of high priority in ecophysiological research. Traditional methods of digestive physiology, however, appear unsuitable for most ecological applications due to lethality or complexity of the procedure.Here, we test the reliability of a simple, cheap, and noninvasive procedure, an acid steatocrit that assesses fat content in feces. It is based on centrifugation of a fecal sample, diluted in acid medium, in hematocrit capillary tube and quantifying the percentage of fat in fecal matter. The method has been previously validated in humans and mice; here, we apply it for the first time in birds.When applied to captive wild‐caught greenfinches, the method showed reasonable internal consistency (r
s = 0.71 for steatocrit values, sampled from the same fecal aliquot in duplicate but processed separately). Individual steatocrit values were significantly repeatable in time in different intervals from eight to at least 20 days (r
s = 0.32–0.49). The relationship between intestinal health and steatocrit values was tested by experimental manipulations. Medication against coccidiosis (a naturally pervasive intestinal infection) reduced, and experimental infection with heterologous coccidian strains increased steatocrit. Individual changes in steatocrit correlated negatively with changes of two markers of nutritional state—plasma triglyceride levels and body mass.Findings of this study suggest that steatocrit has a wide application potential as a marker of intestinal health in ecophysiological research. In particular, we see the perspective of this method for increasingly popular immunoecological research, conservation medicine, and studies of animal coloration.