This study aimed to evaluate the effect of boiling seeds of three cowpea (Vigna unguiculata) varieties on nutrient ileal and total tract digestibilities in rats and in vitro hindgut production of short-chain fatty acids (SCFAs). Boiling influenced nutrient ileal and total tract digestibilities, and production of SCFAs (P < 0.05), but its effect was in general cowpea specific. For instance, boiling increased the apparent ileal proline digestibility of red-hulls cowpea only (P < 0.05), while it only increased the apparent total tract cellulose digestibility of pink-hulls cowpea (P < 0.05). White-hulls cowpea had in general higher nutrient apparent ileal and total tract digestibilities (P < 0.05). For instance, white-hulls cowpea had greater (+2.6% units) apparent total tract dry matter digestibility than pink- and red-hulls cowpeas (P < 0.05). In conclusion, boiling influenced several parameters relate to the nutritional value of the cowpeas, but its effect was specific for each cowpea variety. White-hull cowpea had the highest nutritional value.