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Quantum key distribution over probabilistic quantum repeaters is addressed. We compare, under practical assumptions, two such schemes in terms of their secret key generation rates per quantum memory. The two schemes under investigation are the one proposed by Duan et al. [Nature (London) 414, 413 (2001)] and that of Sangouard et al. [ Phys. Rev. A 76, 050301 (2007)]. We consider various sources of imperfection in both protocols, such as nonzero double-photon probabilities at the sources, dark counts in detectors, and inefficiencies in the channel, photodetectors, and memories. We also consider memory decay and dephasing processes in our analysis. For the latter system, we determine the maximum value of the double-photon probability beyond which secret key distillation is not possible. We also find crossover distances for one nesting level to its subsequent one. We finally compare the two protocols in terms of their achievable secret key generation rates at their optimal settings. Our results specify regimes of operation where one system outperforms the other. [ABSTRACT FROM AUTHOR]