We aimed to investigate the relationship between influenza infection and invasive pneumococcal disease (IPD) in Ontario, Canada, using several complementary methodological tools. We evaluated the relationship between the seasonal wave forms for influenza and IPD using fast Fourier transforms in order to examine the relationship between these epidemic waveforms over yearly timescales, i.e., to test the hypothesis that influenza influences IPD by enhancing person-to-person transmission. We also used three complementary statistical methods (time-series methods, negative binomial regression, and case-crossover methods) to evaluate the short-term effect of influenza dynamics on pneumococcal risk, i.e., to examine whether the risk of IPD is increased in previously colonized individuals.