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ENCePP Guide on Methodological Standards in Pharmacoepidemiology



The Guide on Methodological Standards in Pharmacoepidemiology offers a single web resource for methodological English language guidance in pharmacoepidemiology. For each topic covered, direct electronic access is given to internationally agreed recommendations, and key points from important guidelines, published articles and textbooks are highlighted. Where relevant, gaps in existing guidance are addressed with what ENCePP considers good practice. 

The current version of the Guide is Revision 6, dated July 2017.


The 6th Revision of the Guide on Methodological Standards in Pharmacoepidemiology includes revisions, amendments and new references in all the chapters. Revisions were performed by the authors, in collaboration with the editorial group. External comments received were also considered.


Due to developments in some areas or need for restructuring and clarification, there have been more important changes in the following chapters:

  • 3. Development of the study protocol
  • 4.6. Research networks
  • 5.2. Bias and confounding
  • 5.6. Pragmatic trials and large simple trials
  • 7. Quality management
  • 9.2. Scientific integrity and ethical conduct


The following chapters were newly added:

  • 1. Introduction
  • 4.3. Patient registries
  • 4.1.1. Surveys


Annex 1. to the Guide provides methodological guidance addressing the conduct of systematic reviews and meta-analyses of drug safety endpoints generated in completed (published or unpublished) comparative pharmacoepidemiological studies.

The Guide is updated annually by structured review to maintain its dynamic nature. It may also be amended as necessary in response to comments received. For this purpose, any comment and additional relevant guidance document may be forwarded to

Relevant documents:


Individual Chapters:


1. Introduction

2. Formulating the research question

3. Development of the study protocol

4. Approaches to data collection

4.1. Primary data collection

4.1.1. Surveys

4.1.2. Randomised clinical trials

4.2. Secondary data collection

4.3. Patient registries

4.3.1. Definition

4.3.2. Conceptual differences between a registry and a study

4.3.3. Methodological guidance

4.3.4. Registries which capture special populations

4.3.5. Disease registries in regulatory practice and health technology assessment

4.4. Spontaneous report database

4.5. Social media and electronic devices

4.6. Research networks

4.6.1. General considerations

4.6.2. Models of studies using multiple data sources

4.6.3. Challenges of different models

5. Study design and methods

5.1. Definition and validation of drug exposure, outcomes and covariates

5.1.1. Assessment of exposure

5.1.2. Assessment of outcomes

5.1.3. Assessment of covariates

5.1.4. Validation

5.2. Bias and confounding

5.2.1. Selection bias

5.2.2. Information bias

5.2.3. Confounding

5.3. Methods to handle bias and confounding

5.3.1. New-user designs

5.3.2. Case-only designs

5.3.3. Disease risk scores

5.3.4. Propensity scores

5.3.5. Instrumental variables

5.3.6. Prior event rate ratios

5.3.7. Handling time-dependent confounding in the analysis

5.4. Effect measure modification and interaction

5.5. Ecological analyses and case-population studies

5.6. Pragmatic trials and large simple trials

5.6.1. Pragmatic trials

5.6.2. Large simple trials

5.6.3. Randomised database studies

5.7. Systematic reviews and meta-analysis

5.8. Signal detection methodology and application

6. The statistical analysis plan

6.1. General considerations

6.2. Statistical analysis plan structure

6.3. Handling of missing data

7. Quality management

8. Dissemination and reporting

8.1. Principles of communication

8.2. Communication of study results

9. Data protection and ethical aspects

9.1. Patient and data protection

9.2. Scientific integrity and ethical conduct

10. Specific topics

10.1. Comparative effectiveness research

10.1.1. Introduction

10.1.2. General aspects

10.1.3. Prominent issues in CER

10.2. Vaccine safety and effectiveness

10.2.1. Vaccine safety

10.2.2. Vaccine effectiveness

10.3. Design and analysis of pharmacogenetic studies

10.3.1. Introduction

10.3.2. Identification of generic variants

10.3.3. Study designs

10.3.4. Data collection

10.3.5. Data analysis

10.3.6. Reporting

10.3.7. Clinical practice guidelines

10.3.8. Resources

Annex 1. Guidance on conducting systematic revies and meta-analyses of completed comparative pharmacoepidemiological studies of safety outcomes