Cre complementation is a process of reconstitution of the activity of DNA recombinase by noncovalent association of multiple segments of Cre recombinase, which are enzymatically inactive by themselves. Cre complementation is potentially useful in restriction of Cre activity in a specific subset of cells, with temporal regulation, by limiting overlap in expression of Cre fragments. We analyzed the efficiency of Cre complementation using three different dimerizing modules in the context of non-neuronal cells and found differential Cre complementation efficiency. We further tested the efficiency of Cre complementation in primary hippocampal neurons derived from transgenic mice harboring a reporter gene flanked by loxP sites and confirmed differential activity of dimerization modules in Cre-dependent recombination of the transgene. These results suggest possible application of dimerizer-based Cre complementation in inducible expression/inactivation of target genes in a specific subset of neurons in the complex environment of nervous tissue in vivo.