When to Choose IHC over H&E Staining: A Comprehensive Guide

By HistoWiz Staff
March 12th, 2024

In the realm of pathology and histology, two common techniques reign supreme in tissue staining: Hematoxylin and Eosin (H&E) staining and Immunohistochemistry (IHC). Both methods serve crucial roles in diagnosing and understanding various diseases and conditions. However, knowing when to opt for one over the other can significantly impact diagnostic accuracy and treatment decisions. In this guide, we'll delve into the nuances of each technique and explore the scenarios where choosing IHC over H&E staining is warranted.

Understanding H&E Staining

H&E staining is a cornerstone technique in histopathology. It involves using hematoxylin to stain cell nuclei blue and eosin to stain cytoplasm and extracellular structures pink. This traditional staining method provides excellent morphological detail, allowing pathologists to visualize tissue architecture and identify cellular abnormalities.

Limitations of H&E Staining:

Despite its widespread use, H&E staining has several limitations that may hinder diagnostic accuracy:

  1. Lack of Specificity: H&E staining provides morphological information but lacks specificity in identifying certain cellular components or molecular markers associated with specific diseases.
  2. Inability to Differentiate Cell Types: While H&E staining can distinguish between basic tissue structures, it may not always differentiate between cell types with similar morphological features.
  3. No Detection of Protein Expression: H&E staining cannot detect specific protein expression patterns or identify protein localization within tissues, so it is not an option if your study relies on assessing localization of molecular markers.

The Power of Immunohistochemistry (IHC)

In contrast to H&E staining, IHC utilizes antibodies to target specific proteins within tissue samples. This technique enables the visualization of protein expression patterns. By targeting proteins associated with various diseases, IHC enhances diagnostic accuracy and facilitates personalized treatment strategies.

When to Choose IHC over H&E Staining

  1. Identification of Specific Biomarkers: In cases where specific protein markers are indicative of disease pathology, IHC offers unparalleled specificity. For instance, in cancer diagnosis, IHC can detect hormone receptors (e.g., estrogen receptor, progesterone receptor) and molecular markers (e.g., HER2/neu) crucial for determining treatment options.
  2. Differentiating Between Histological Subtypes: Some diseases present with histological variations that are not easily discernible with H&E staining alone. IHC can aid in distinguishing between subtypes of tumors or identifying particular cell lineages, contributing to more accurate diagnoses and prognoses.
  3. Confirmation of Suspected Diagnoses: When H&E staining yields inconclusive or ambiguous results, IHC can provide confirmatory evidence. By targeting specific antigens associated with suspected diseases, IHC can validate initial diagnostic impressions and guide subsequent treatment strategies.
  4. Assessment of Tumor Proliferation and Invasion: IHC staining for proliferation markers such as Ki-67 can assess tumor aggressiveness and predict patient outcomes. Additionally, IHC staining for proteins involved in epithelial-mesenchymal transition (EMT) can help evaluate tumor invasion and metastatic potential.
  5. Evaluation of Treatment Response: IHC plays a vital role in monitoring response to therapy by assessing changes in protein expression patterns over time. For example, in patients undergoing targeted therapy or immunotherapy, IHC can track alterations in drug targets or immune cell infiltration, guiding treatment adjustments as needed.
  6. Detection of Infectious Agents: In infectious diseases, IHC can identify the presence of specific pathogens within tissue samples. By targeting microbial antigens, IHC aids in the diagnosis of infectious conditions such as viral, bacterial, or fungal infections.


While H&E staining remains a fundamental tool in histopathology, the advent of immunohistochemistry has revolutionized diagnostic capabilities. By leveraging the specificity of antibody-antigen interactions, IHC provides invaluable insights into disease pathology, aiding in accurate diagnosis, prognostication, and treatment decision-making. Knowing when to choose IHC over H&E staining is essential for optimizing patient care and achieving precise pathological diagnoses.

In summary, consider incorporating immunohistochemistry into your diagnostic arsenal when faced with cases requiring:

  • Identification of specific biomarkers
  • Differentiation between histological subtypes
  • Confirmation of suspected diagnoses
  • Assessment of tumor proliferation and invasion
  • Evaluation of treatment response
  • Detection of infectious agents

By harnessing the power of IHC, pathologists can unlock new dimensions of tissue analysis, paving the way for more personalized and effective patient management strategies. If you want to learn more about how HistoWiz can help with your IHC needs, please contact us here.