R-parity violation is getting more attention as a possible alternative to natural supersymmetry in the current LHC searches. We investigate whether the baryon asymmetry of the universe is explained in the framework of the supersymmetric extension of the Standard Model with R-parity violating interactions. It is shown that the Affleck-Dine mechanism naturally works via a trilinear interaction $LLE^c$, $LQD^c$, or $U^cD^cD^c$, if the magnitude of the coupling corresponding to the operator $¥lambda$, $¥lambda'$, or $¥lambda''$ is sufficiently small. The formation of Q-balls and their subsequent evolution are also discussed. The parameter region is constrained by considering the wash out effect due to the sphaleron transitions and baryon/lepton number violating interactions induced by R-parity violating operators, and the requirement that the hadronic decay of unstable LSPs must not affect the observed light element abundance. It is found that the present baryon asymmetry can be explained in the parameter region where R-parity is mildly violated and the mass of the gravitino is relatively heavy. On the other hand, it is difficult to explain the present baryon asymmetry for larger values of R-parity violating couplings, since Q-balls are likely to be destructed in the thermal environment and the primordial baryon number is washed away.