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Purpose: To investigate the structure–function relationship in eyes with drusen with mesopic and scotopic microperimetry. Methods: We analyzed structural and functional data from 43 eyes with drusen. Functional data were acquired with mesopic and scotopic two-color (red and cyan) microperimetry. Normative values were calculated using data from 56 healthy eyes. Structural measurements were green autofluorescence and dense macular optical coherence tomography scans. The latter were used to calculate the retinal pigment epithelium elevation (RPE-E) and the photoreceptor reflectivity ratio (PRR). The pointwise structure–function relationship was measured with linear mixed models having the log-transformed structural parameters as predictors and the sensitivity loss (SL, deviation from normal) as the response variable. Results: In the univariable analysis, the structural predictors were all significantly correlated (P < 0.05) with the SL in the mesopic and scotopic tests. In a multivariable model, mesopic microperimetry yielded the best structure–function relationship. All predictors were significant (P < 0.05), but the predictive power was weak (best R2 = 0.09). The relationship was improved when analyzing locations with abnormal RPE-E (best R2 = 0.18). Conclusions: Mesopic microperimetry shows better structure–function relationship compared to scotopic microperimetry; the relationship is weak, likely due to the early functional damage and the small number of tested locations affected by drusen. The relationship is stronger when locations with drusen are isolated for the mesopic and scotopic cyan test. Translational Relevance: These results could be useful to devise integrated structure–function methods to detect disease progression in intermediate age-related macular degeneration. ; DPC and GM received funding from the Innovative Medicines Initiative 2 Joint Undertaking under grant 116076 (Macustar). This joint undertaking receives support from the European Union's Horizon 2020 research and innovation program ...