Background: Randomized Clinical Trials (RCTs) are important tools to establish the effects of a given intervention. Investigators should focus on outcomes that patients perceive: patient-important outcomes (PIOs), clinical endpoints that patients value directly and reflect how they feel, function, or survive. However, it is easier to consider surrogated outcomes to reduce costs and achieve better-looking results. The problem with these outcomes is that they indirectly measure PIOs, which might not correlate linearly or translate reliably into a positive PIO. Methods: We systematically searched MEDLINE for atopic disease RCTs rated among the top 10 allergic diseases and general internal medicine journals from the last 10 years. Two independent reviewers worked in duplicate and independently to collect data from all eligible articles. We gathered information regarding the type of study, title, author information, journal, intervention type, atopic disease, and primary and secondary outcomes. We assessed the outcomes investigators used in RCTs of atopic diseases and asthma. Results: This quantitative analysis included n = 135 randomized clinical trials. The most studied atopic disease during the period selected was asthma (n = 69), followed by allergic rhinitis (n = 51). When divided by atopic disease, primary outcomes in RCTs valuing allergic rhinitis had the most significant proportion of PIOs (76.7), asthma surrogated outcomes (38), and asthma/allergic rhinitis laboratory outcomes (42.9). PIOs in allergic rhinitis trials had the most significant proportion of PIOs favoring the intervention (81.4), asthma had the greatest proportion of surrogated outcomes (33.3), and asthma/allergic rhinitis laboratory outcomes (40). When divided by atopic disease, trials studying atopic dermatitis and urticaria had the same proportion of PIOs (64.7) as their secondary outcomes. Asthma had the highest (37.5) surrogate outcomes. Journals of general/internal medicine had a greater proportion of PIOs, and a post hoc analysis showed a significant difference in the proportion and secondary outcomes that favored the intervention between PIOs and laboratory outcomes. Conclusion: Approximately 7.5 out of 10 primary outcomes in RCTs published in general/internal medicine are PIOs compared to 5 out of 10 primary outcomes in atopic disease journals. Investigators should focus on selecting patient-important outcomes in their clinical trials to establish clinical guidelines with better-quality recommendations that impact patients' life and values. Registration: International Prospective Register of Systematic Reviews (PROSPERO, NIHR) ID: CRD42021259256.