We have conducted a detailed analysis of the spatial-temporal characteristics of the A/H1N1 influenza pandemic in May- December 2009 at two levels of spatial aggregation, relying on a large sample of 18,139 laboratory confirmed cases and 22,994 ILI cases collected by a national epidemiological and virological surveillance system. We found substantial spatial variation in pandemic patterns across Peru, with two pandemic waves of A/ H1N1 cases of varying timing and impact across geographic The serial interval is assumed to be exponentially distributed or fixed, with a mean of three or four days. The epidemic growth phase used to estimate the reproduction number consisted of 12 days for the greater Lima metropolitan area (May 31 to June 11) and 16 for the rest of Peru (June 10 to June 25). See Figure F in Text S1 for exact time periods considered as part of the epidemic growth phase. doi:10.1371/journal.pone.0021287.t002