Huntington's disease (HD) is an inheritable degenerative disease of the brain characterized by progressive neural dysfunction and degeneration in the striatum and cerebral cortex, resulting in abnormal motor- and cognitive function, emotional disturbances and premature death. While considerable knowledge has been gained about the pathophysiological mechanisms of HD, curative treatment is still not available. For further elucidation of the pathological processes and identification of potential targets for therapeutic interventions, experimental investigations in animal models are necessary. Transgenic rats in which a truncated HD gene has been inserted, develop progressive HD-like behavioural changes, and thus represent a promising model for experimental investigations of HD. It remains uncertain to what extent striatal neurodegeneration is present in these rats, and it is therefore important to evaluate this quantitatively. Quantitative assessment of cellular populations is typically obtained using a stereological method. In order to select an appropriate stereological study designs for such investigations, the objective of the present study has been to establish a procedure for quantifying striatal cell numbers in thionin stained sections in the rat brain. A non-systematic literature review, combined with snowball sampling, was conducted to retrieve original articles and review of interest and to delineate a suitable design and protocol. This protocol was tested on a limited material of thionin stained sections from a transgenic HD-rat and wildtype littermate control. The optical fractionator protocol was found to be the most suitable in the objective of population estimation, and a set of recommended sampling parameters were identified. We conclude that the proposed Optical Fractionator protocol is suitable to quantitatively test the hypothesis that striatal neurons degenerate in transgenic HD rats.