The intradermal test (IDT) has been developed for confirming diagnosis of canine atopic dermatitis (CAD). Prior to performing IDT, rapid immunoassay (Allercept E-screen 2nd generation; ES2G) can detect allergen-specific immunoglobulin E (IgE) antibodies in canine serum. The objective of this study was to evaluate agreement between IDT and immunoassay in diagnosis of CAD in domestic atopic dogs. Forty dogs were diagnosed with CAD in accordance with Favrot’s criteria. Intradermal testing was performed using 39 selected allergens. ES2G detected IgE antibodies specific for three allergen groups, including indoor allergens, grasses and weeds, and trees. Among 19 dogs diagnosed by IDT, the highest positivity was observed in house dust mites, followed by molds, epidermis and inhalants, house dust, and weeds. A total of 28 atopic dogs were evaluated by rapid ES2G immunoassay. Indoor allergens showed the strongest positive reaction, followed by grasses/weeds and trees. IDT and ES2G were performed concurrently in 17 dogs. The results of ES2G showed slight agreement with those of IDT. Level of agreement was highest for indoor allergens, which showed a predictive positive value of 100% in ES2G. These results indicate that a rapid immunoassay may be valuable for predicting the results of IDT in atopic dogs sensitized to indoor allergens.