We recently identified 1alpha,25-dihydroxy-3-epi-vitamin D3 as a major in vitro metabolite of 1alpha,25-dihydroxyvitamin D3, produced in primary cultures of neonatal human keratinocytes. We now report the isolation of 1alpha,25-dihydroxy-3-epi-vitamin D3 from the serum of rats treated with pharmacological doses of 1alpha,25-dihydroxyvitamin D3. 1alpha,25-dihydroxy-3-epi-vitamin D3 was identified through its co-migration with synthetic 1alpha,25-dihydroxy-3-epi-vitamin D3 on both straight and reverse phase high performance liquid chromatography systems and by mass spectrometry. Along with 1alpha,25-dihydroxy-3-epi-vitamin D3, other previously known metabolites, namely, 1alpha,24(R),25-trihydroxyvitamin D3, 1alpha,25-dihydroxy-24-oxo-vitamin D3 and 1alpha,25-dihydroxyvitamin D3-26,23-lactone, were also identified. Thus, our study for the first time provides direct evidence to indicate that 1alpha,25-dihydroxy-3-epi-vitamin D3 is an in vivo metabolite of 1alpha,25-dihydroxyvitamin D3 in rats.