Many human genes have been mapped precisely in the genome. These genes vary from a few kb to more than 1 Mb in length. Previously, we measured replication timing along the entire lengths of human chromosomes 11q and 21q at the sequence level. In the present study, we used the newest information for human chromosomes 11q and 21q to analyze the replication timing of 30 extremely large genes (>250 kb) in two human cell lines (THP-1 and Jurkat). The timing of replication differed between the 5'- and 3'-ends of each of extremely large genes on 11q and 21q, and the time interval between their replication varied among genes of different lengths. The large genes analyzed here included several tissue-specific genes associated with neural diseases and genes encoding cell adhesion molecules: some of these genes had different patterns of replication timing between the two cell lines. The amyloid precursor protein gene (APP), which is associated with familial Alzheimer's disease (AD1), showed the largest difference in timing of replication between its 5'- and 3'-ends in relation to gene length of all the large genes studied on 11q and 21q. These extremely large genes were concentrated in and around genomic regions in which replication timing switches from early to late on both 11q and 21q. The differences of replication timing between the 5'- and 3'-terminal regions of large genes may be related to the molecular mechanisms that underlie tissue-specific expression.