Gene therapy is a new therapeutic modality that holds vast potential for the treatment of genetic disorders. Retroviruses are used as a vehicle for the transfer of genes into mammalian cells. The process of gene transfer has been shown to depend on the cell cycle status of target cells. We constructed a mathematical model that integrates the kinetics of gene transfer with cell cycle kinetics. We define three cell populations: uninfected cells, cells with the virus in their cytoplasm, but not integrated, and infected cells, in which the viral DNA has integrated in their genome. Our model predicts that the stability of the viral particles after internalization in the cellular cytoplasm, limits the process of gene transfer. Intracellular viral half-life also limits the usefulness of synchronization experiments, used to detect cell cycle dependence of the gene transfer process. We use the predictions of our model to propose a new experimental method for the detection of cell cycle dependence of retrovirus mediated gene transfer. It is based on the maturity distributions of the infected cells, and it is independent of viral intracellular stability. Despite the importance of the viral intracellular half-life this quantity still remains unknown. An extended version of the model is used to simulate a novel experimental method that measures the intracellular retroviral half-life. Analytical solutions of a simplified model confirm our numerical results and reveal the key dimensionless groups that characterize the process of gene transfer. Knowledge of the intracellular half-life of retroviral vectors is of particular importance for the design of new vectors, especially for slowly growing target cells, such as the stem cells of the hematopoietic system.