The aim of this study was to compare the effects of two Se sources on the early lactation of native goats, on nutrient digestibility, as well as nitrogen and energy status of Iranian native goats. Twenty-one native goats aged, approximately 41 ± 9 months and having body weights of 46 ± 8 kg were selected for the experiment. The goats were randomly divided into three groups with an equal number of goats. One group was supplemented with Selemax 2000® as the organic selenium (OS), the second group received diluted sodium selenite as the inorganic selenium, while the third group received no supplementation and served as the control group (C). The results of this research showed that the selenium supplement did not have a significant effect on nutrient digestibility (apart from crude fat) (P > .05) but, the dry matter, organic matter and crude protein intake significantly increased. However, faecal N, urinary N, total N production and energy status were affected by the treatments (P < .05). It can be concluded that OS seems to be a better choice, considering the nitrogen and energy available for metabolism and its partition between milk production and deposit/mobilization within the body.