The mammalian Y chromosome contains genes important for male sexual maturity and reproduction. The mouse Y chromosome long arm harbours a number of multi-copy genes whose absence or reduced representation has been linked to sperm defects and offspring sex ratio distortion in favour of females. Understanding the biological mechanisms of sex ratio distortion and related sperm aberrations could not only result in benefits for fertility research, but also in the development of methods for large scale animal breeding pre-implantation sex selection. The distortion has been linked to an intragenomic conflict between the X and Y chromosomes that impacts spermiogenesis. Since the proportion of X- and Y-bearing sperm does not differ in affected animals, and there is no selective destruction of male embryos post-fertilisation, a functional difference must exist between the X- and Y-bearing sperm. This thesis describes the investigation into the physiological and molecular mechanisms of a large Y-chromosome long arm deletion in the mouse model MF1XYRIIIqdel. The examination of physiological characteristics revealed a distinct sperm morphology within the deletion model. Detailed characterisation of sperm shape demonstrated that aberrations consistently occur within specific regions of the sperm head, linking the distorted morphology to particular maturation stages in the sperm cycle. Using sperm fluorescence in situ hybridisation, a novel and detailed comparison of X- and Y- bearing sperm has shown that a subtle distinction in shape also exists between the X- and Y- bearing sperm in the deletion model. Breeding data were examined and showed a skew towards female offspring and a slightly reduced litter size. Sperm enzyme activity assays did not reveal altered hyaluronidase activity in MF1XYRIIIqdel sperm. Physiological differences between X- and Y- bearing sperm must result from differential gene expression, complicated by the syncitial nature of sperm development. To explore this, a detailed molecular characterisation of the MF1XYRIIIqdel phenotype in developing haploid spermatids was performed. Cellular elutriation and fractionation techniques were employed to separate spermatids at different stages of maturation and isolate different subcellular compartments. Differences in the transcriptional profile between these populations were analysed by microarray and RNA sequencing analysis of total and micro RNA. This work yielded a collection of coding and non-coding transcripts which show distinctive expression and compartmentalisation differences between the deletion model and its wild-type counterpart across several sperm maturation stages. Combining these strategies has led to the identification of several gene products potentially implicated in observed physiological differences and the offspring sex ratio skew, providing candidate genes for further research.