Due to the chicken’s (Gallus gallus domesticus Linnaeus, 1758) importance as a model organism and for agriculture, the whole genome assembly was published in 2004. Despite international efforts and many improvements, 138 Mb upon 1.21 Gb are still not assigned to chromosomes (virtual Chromosome Unknown), six microchromosomes remain absent (Gallus_gallus-5.0), and three have a partial coverage. In order to contribute to the sequencing of microchromosomes, we decided to select six BAC clones showing painting signal by FISH on microchromosomes, thus probably containing repeated sequences potentially absent in the assembly. We performed sequencing with a Pacific Bioscience RSII equipment (P4C6 chemicals). DNA extraction is a crucial step, as both high quantity and quality are needed for Pacbio sequencing. We obtained end sequences for the six BACs before pooling them in the smart cell. As expected, we obtained long reads (9 Kb) and high sequencing depth (953X). Three of these BACs were particularly resistant to sequencing and had to be sequenced separately, demonstrating that some sequence biases could be a possible explanation for the low coverage of microchromosomes in whole genome approaches. The contigs were established using different assembler: HGAP3, Miniasm, MHAP and Canu. The vector was cleaned, the presence of Escherichia coli Migula, 1895, DNA was filtered and the contigs assigned using the Bac end sequences. The best results were obtained with HGAP3 but Miniasm gave very interesting results with some of the repeated sequences. The alignment against Gallus_gallus-5.0 has allowed to assign some of the Unknown contigs to microchromosomes.