Platelet-activating factor (PAF) mediates an array of biological processes in the mammalian central nervous system as a bioactive lipid messenger in synaptic function and dysfunction (plasticity, memory, and neurodegeneration). The intracellular enzyme that deacetylates the PAF (PAFAH1B) is composed of a tetramer of two catalytic subunits, ALPHA1 (PAFAH1B3) and ALPHA2 (PAFAH1B2), and a regulatory dimer of LIS1 (PAFAH1B1). We have investigated the mouse PAFAH1B subunit genes during brain development in normal mice and in mice with a hypomorphic allele for Lis1 (Lis1/sLis1; Cahana et al.  Proc Natl Acad Sci U S A 98:6429–6434). We have analyzed quantitatively (by means of real-time polymerase chain reaction) and qualitatively (by in situ hybridization techniques) the amounts and expression patterns of their transcription in developing and postnatal brain, focusing mainly on differences in two laminated encephalic regions, the forebrain (telencephalon) and hindbrain (cerebellum) separately. The results revealed significant differences in cDNA content between these two brain subdivisions but, more importantly, between the LIS1 complex subunits. In addition, we found significant spatial differences in gene expression patterns. Comparison of results obtained with Lis1/sLis1 analysis also revealed significant temporal and spatial differences in Alpha1 and Lis1 expression levels. Thus, small changes in the amount of the Lis1 gene may differentially regulate expression of Alpha1 and Alpha2, depending on the brain region, which suggests different roles for each LIS1 complex subunit during neural differentiation and neural migration. J. Comp. Neurol. 520:3877–3894, 2012. © 2012 Wiley Periodicals, Inc.