Objective To systematically evaluate the efficacy of Houttuynia cordata Injection (HI) in treating respiratory system diseases, such as infection of the upper respiratory tract, pneumonia and respiratory tract infection, so as to provide references for revaluation after having access to market and its rational use. Methods The literatures concerning both randomized controlled trials (RCTs) and clinical control study of HI were searched in PUBMED, EMBASE, Chinese Biomedical Disc (CBMdisc), Chinese National Knowledge Infrastructure (CNKI), Chinese Science and Technology Journal Full-text Database (VIP) from 1979 to December of 2010. The quality assessment and data extraction for RCTs were conducted by two reviewers independently. Meta-analyses were conducted with the Cochrane Collaboration’s RevMan 5.0 software. Results a) Fifty-three trials including 46 RCTs and 7 non-RCTs were included, the quality grade was generally lower from 2 to 6 scores: 24 trials scored 5, 11 trials scored 3, 7 trials scored 4, 2 trials scored 6, and the rest 9 trials scored 2; b) There were 7481 patients (2520 adult and 4961 children) with infection of the upper respiratory tract, pneumonia, or respiratory tract infection. The interventions in the treatment group were Houttuynia cordata Injection or the joint of Houttuynia cordata Injection and support measures. The control group included four categories: Antiviral, Antibiotics, the joint of Antiviral and Antibiotics, and Chinese medicine injection (CMI). Both the total effective rate and average defervescence days were regarded as the result indexes; c) In all adult trials, when HI was used alone to treat the infection of upper respiratory tract (compared with the control group of antiviral, antibiotics, and the joint of antiviral and antibiotics), the pneumonia (compared with the control group of antiviral, and antibiotics), and the respiratory tract infection (compared with the control group of antibiotics, and CMI), the differences between the treatment group and the control groups were significant different, and the total effective rate of the treatment groups was higher than that of the control groups. The average defervescence days of the treatment groups were one to one and a half days shorter than those of the control groups; and d) In children trials, compared with the three control groups of antiviral, antibiotics, and CMI for treating infection of upper respiratory tract, the pneumonia, and the respiratory tract infection, respectively, the total effective rate was similar in the treatment group without significant difference. The left groups corresponding to those in the adult trials also showed a certain effects. Conclusion Houttuynia cordata Injection for adult respiratory system diseases tends to have a good effect, and indicates the effect of rapid defeverscence, so it is still recommended in clinic with the cautions of rational use and ADR/AE supervision. There is no evidence to fully prove its safety and effectiveness although HI is widely used for children, so it is advisable to “stop using it for children”. It needs to carry out more new precise clinical trials to provide high-quality evidence.