Alternaria brown spot, caused by Alternaria alternata, recently appeared in Brazil and is now causing serious damage to Murcott tangors in São Paulo State. The Alter-Rater model and other systems for timing fungicide applications as well as different fungicide programs were evaluated in two seasons in different citrus-growing areas of São Paulo State. Alternaria brown spot severely reduced yields of Murcotts in the unsprayed controls in both years. Fungicide applications reduced fruit drop and increased yields in many cases. Regression analyses showed that yield declined as disease severity increased. A copper fungicide applied according to the Alter-Rater model with a trigger value of 50 required one to two more applications than a calendar program in both locations in 2002–03. Use of the Alter-Rater 50 increased the number of fruit harvested in both locations, but did not improve fruit quality when compared to the calendar program. Use of the Alter-Rater with trigger values of 100 or 150, or the Copper model forecast fewer sprays and resulted in poor disease control and low yields. In a test in 2003–04, fungicide applications timed with the Alter-Rater 50 were no more effective than calendar sprays. Copper fungicides throughout the season or programs with copper applied early followed by dithiocarbamates or QoI fungicides later provided better disease control than a full-season mancozeb program. Murcott product in some citrus growing areas in Brazil will be possible only if the value of the crop is sufficient to justify 10 or more fungicide applications per year.