BackgroundClassical allergy diagnostic workup “from symptoms to molecules” comprises 1) clinical investigation, 2) skin prick- and IgE- testing, and recently, 3) molecular allergy testing. We aimed to examine the diagnostic fidelity of the alternative approach “from molecules to symptoms”, which was recently suggested in the EAACI Molecular Allergology User’s Guide, in a retrospective clinical study.MethodsRecords from 202 patients with clinically suspected allergic sensitizations were extracted from files at two sites applying either the “ISAC-first” workup with IgE-testing by immuno-solid phase allergen chip ISAC112 followed by selected skin prick tests (SPT) or the “SPT-first” starting with SPT followed by the microarray test.ResultsIn the ISAC-first procedure significantly less SPTs were performed during allergy diagnosis (median 4 vs. 14). By SPT in 19% of patients in the ISAC-first group and in 34% in the SPT-first group additional respiratory allergens (p = 0.014) were detected not positive in ISAC microarray. By ISAC microarray test 18% additional sensitizations were found in the ISAC-first, and 32% in SPT-first cohort (p = 0.016). For food allergens 13 and 12% additional sensitizations were detected by the microarray not detected by SPT in the two groups (p = 0.800). No additional food allergen was found by SPT in the ISAC-first group, while in 6% of the cases in the SPT-first group detected sensitizations were negative in the microarray.DiscussionThe ISAC-first approach followed by (fewer) SPTs meets the demands for a patient’s tailored diagnostic work-up and therefore can be considered equivalent to the conventional way using the skin prick test as first screening tool, followed by IgE diagnosis.ConclusionsFor the diagnostic verification of clinically suspected allergy, the novel concept “from molecules to clinic” offers a reliable diagnostic workup in shorter time. Due to lower skin test numbers it is especially applicable for young children and seniors, in atopic patients, and whenever skin tests get difficult or unreliable.Electronic supplementary materialThe online version of this article (10.1186/s40413-018-0199-y) contains supplementary material, which is available to authorized users.