Stem end rot (SER) caused by Botrytis cinerea is the primary postharvest disease in the Chilean kiwifruit industry. Relationships between the postharvest occurrence of SER in ‘Hayward’ kiwifruit and the temporal dynamics of earlier B. cinerea colonization of the floral parts (petals, sepals, receptacles, styles) was studied in five orchards over two consecutive seasons in Chile. Weather conditions in the first season favored B. cinerea infection with roughly constant colonization of floral parts up to about 120 days after full bloom, but colonization then increased up until harvest. In the second season, colonization was roughly constant throughout. Latent infections of the fruit occurred in both seasons but were high in the first season and low in the second. Incidence of latent infections at harvest were the best predictors (r > 0.8) of postharvest SER. The number of preharvest infection periods calculated using temperature, leaf wetness, and relative humidity satisfactorily predicted SER incidence by an exponential model, R2 = 0.90, P < 0.001. Results indicated environmental variables play key roles in the temporal dynamics of B. cinerea colonization. Quantification of latent B. cinerea infections in asymptomatic fruit close to harvest, is a practicable way to predict later incidence of SER during storage.