Evaluating clustering results is a fundamental task in microarray data analysis, due to the lack of enough biological knowledge to know in advance the true partition of genes. Many quality indexes for gene clustering evaluation have been proposed. A critical issue in this domain is to compare and aggregate quality indexes to select the best clustering algorithm and the optimal parameter setting for a dataset. Furthermore, due to the huge amount of data generated by microarray experiments and the requirement of external resources such as ontologies to compute biological indexes, another critical issue is the performance decline in term of execution time. Thus, the distributed computation of algorithms and quality indexes becomes essential. Addressing these issues, this paper presents the MicroClAn framework, a distributed system to evaluate and compare clustering algorithms using the most exploited quality indexes. The best solution is selected through a two-step ranking aggregation of the ranks produced by quality indexes. A new index oriented to the biological validation of microarray clustering results is also introduced. Several scheduling strategies integrated in the framework allow to distribute tasks in the grid environment to optimize the completion time. Experimental results show the effectiveness of our aggregation strategy in identifying the best rank among different clustering algorithms. Moreover, our framework achieves good performance in terms of completion time with few computational resources.