Imbalance in microbial composition (i.e. dysbiosis) in the gut microbiome is consensually considered an indicator of deteriorated health and has been associated to different chronic health conditions. However, there is no clear evidence how this generalizes to the other human microbiomes. Especially, researches on the relationship between respiratory microbiota imbalance and chronic lung diseases are recent whereas microbial colonization of the airways respiratory tract have characterized chronic lung diseases. Imbalance is mainly measured through the relative abundance of microbial species in space and time within a given community (i.e. alpha-diversity). Identifying a range of values in alpha-diversity when comparing exacerbated, stable patients and healthy subjects may lead to identify new biomarker in chronic respiratory diseases. In the present work, we propose a systematic review of studies investigating the lung microbiota alpha-diversity in patients with chronic respiratory diseases in which a control group based on disease status or healthy subjects is provided for comparison. We focused on the most common measures of alpha-diversity (Chao1, Shannon, and Simpson) indexes and the most common chronic diseases (asthma, chronic obstructive pulmonary disease –COPD-, cystic fibrosis –CF-, bronchiectasis, and pulmonary hypertension). Subsequently, we conducted a meta-analysis based on random-effects models using the R package metafor to characterize the difference in alpha-diversity indexes when comparing cases to controls. We also explored heterogeneity of sources and risk of bias though Factor Analysis of Mixed Data (FAMD) using the FactoMineR R package. After removing duplicate records, we screened 351 articles on title and abstract, of which 27 met our inclusion criteria for the systematic review. Finally, data from 25 studies were used in the meta-analysis. Eight studies deal with CF, 8 with COPD, 10 with asthma and 1 with bronchiectasis. All of the studies dedicated to the respiratory tract microbiota, mainly based on sputum samples analysis and, the majority of the studies used metataxonomy approaches. As highlighted by the meta-analysis, these metataxonomy methods exhibited numerous heterogeneities. Differences in alpha-diversity indexes between healthy and diseased people were observed only in some of the diseases studied. However, prudence is required in its interpretation because of substantial heterogeneity.