Selection of putative transformants is an essential step in transgenic plant development program of important pulse crop pigeonpea. The multiple shoot induction of pigeonpea was studied under the influence of three negative selection agents kanamycin, hygromycin and glufosinate ammonium. Minimum inhibitory concentration of these selection agents on shoot regeneration was determined. These observations were then applied to genetic transformation studies where 100 mg/l kanamycin and 2.0 mg/l glufosinate ammonium were used to select the neomycin phosphotransferase II (nptII) and bar expressing T0pigeonpea transformants, respectively. Hygromycin was found to be detrimental for shoot regeneration in all applied concentrations. T1seeds obtained from nptIIpositive events were screened by incubating 5 h in 100 mg/l kanamycin solution prior to germination. T1events containing bargene were selected by painting 2.0 mg/l solution of glufosinate ammonium on adaxial surfaces of the leaves. Positive transformants survived in both the selection processes, were further confirmed by polymerase chain reaction analysis. Knowledge generated through this study will facilitate the incorporation of agronomically important traits in transgenic pigeonpea for its betterment.