A field experiment was conducted during the rainy (kharif) seasons of 2005, 2006 and 2007 at Agricultural Research Station, Gulbarga, University of Agricultural Sciences; Dharwad (Karnataka) on shallow black soils to study the effect of seed inoculation of biofertilizers in pigeonpea based intercropping systems. The treatment comprised of two intercropping systems viz., pigeonpea + pearlmillet (1:2) and pigeonpea + greengram (1:2) with 10 different integrated fertilizer levels. The seeds were inoculated with suitable Rhizobium strains for pigeonpea and greengram and with Azospirillum for pearlmillet. On the basis of 3 years results, pigeonpea + greengram intercropping systems recorded significantly higher pigeonpea seed yield (14.43 q/ha), pigeonpea equivalent yield (17.13 q/ha), gross returns (` 40,983/ha), net returns (` 32,499/ha) and B: C ratio (3.81) over pigeonpea + pearlmillet intercropping system (13.23 q/ha, 14.78 q/ha, ` 35,483/ha, ` 27,230/ha and 3.29, respectively). The seed yield of pigeonpea, pearlmillet and greengram increased significantly due to combined application of FYM, RDF and biofertilizer as compared to control. Among the integrated fertilizer levels, application of FYM @ 5 t/ha + 100% RDF + seed inoculation of biofertilizers recorded significantly higher pigeonpea yield (15.74 q/ha), pigeonpea equivalent yield (18.29 q/ha), gross returns (`43,930/ha) , net returns (` 34,650/ha) and B:C ratio(3.72) over other INM practices but it was found to be on par with application of FYM @ 5 t/ha + 50% RDF + seed inoculation of biofertilizers (15.38 q/ha, 17.83 q/ha, ` 42,847/ha, ` 34,032/ha and B:C ratio 3.85, respectively).