The purpose of this research study was to study gender based participation in political institutions in Kenya and in Uganda. To achieve this, the study examined the effect of multiparty democracy on gender equality by tracing the history of multi-party democracy in the two countries. Also, this research looks into affirmative action as one of the mechanisms that has been adopted to achieve gender equality in political institutions and whether the formulae adopted by each of the countries are effective. Further, it has sought to analyze the impact of increased level of female representation in political institutions on the gender agenda in Kenya and Uganda. The primary data collection method used for this study was interviews, which were conducted by giving the respondents questionnaires with predetermined questions. Also, telephone conversations were another effective tool of collection for the respondents who were not able to fill in the questionnaire physically. The secondary data collection method used was library searches by studying books and journals that have been written on the research topic. The internet was also used to source previous journals and articles. The findings of the research are that gender inequality persists in political institutions in Kenya and Uganda despite the International instruments and laws that they have put in place. However, the researcher concludes that Uganda has made major strides in ensuring that there is gender parity in the political parties and the parliament.