This paper analyses the role of selected institutional factors on the costs of waste management in the Czech Republic, a country with extreme territorial fragmentation. The analysis is based on two original datasets from 2,065 municipalities. A model is constructed which determines the relevance of selected factors with respect to the unit cost of waste management service and also highlights the differences between 2014 and 2019. The results are, largely extent, similar to the findings of existing international research related to this topic, but with some specificities. Our data show a significant effect of contracting out on cost reduction and a statistically insignificant effect of public mode of production on unit costs. They also suggest that intermunicipal cooperation has a cost-reducing effect, but public-private partnerships, increased market concentration and the provision by multinationals have a cost-increasing effect. The impact of economies of scale on cost reduction is somehow visible but cannot be confirmed, especially for larger scale territories. The data also suggest a possible beginning of a process of remunicipalisation, but the time series is insufficient to demonstrate this trend.