The human genome is arguably the most complete mammalian reference assembly1–3 yet more than 160 euchromatic gaps remain4–6 and aspects of its structural variation remain poorly understood ten years after its completion7–9. In order to identify missing sequence and genetic variation, we sequenced and analyzed a haploid human genome (CHM1) using single-molecule, real-time (SMRT) DNA sequencing10. We closed or extended 55% of the remaining interstitial gaps in the human GRCh37 reference genome—78% of which carried long runs of degenerate short tandem repeats (STRs) often multiple kilobases in length embedded within GC-rich genomic regions. We resolved the complete sequence of 26,079 euchromatic structural variants at the basepair level, including inversions, complex insertions, and long tracts of tandem repeats. Most have not been previously reported with the greatest increases in sensitivity occurring for events less than 5 kbp in size. Compared to the human reference, we find a significant insertional bias (3:1) in regions corresponding to complex insertions and long STRs. Our results suggest a greater complexity of the human genome in the form of variation of longer and more complex repetitive DNA that can now be largely resolved with the application of this longer-read sequencing technology.